3743 results for "RNA AND sequencing OR transcriptome"

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• RNAseq samples of patients with anti-PD-1 resistant HNSCC from a non-randomized, open-label phase 1b clinical trial

  Immune checkpoint blockade (ICB) is an effective treatment for a subset of patients with head and neck squamous cell carcinoma (HNSCC); however, the majority remain refractory. In a nonrandomized, open-label Phase 1b clinical trial, participants with recurrent and/or metastatic (R/M) HNSCC who had progressed on ICB were treated with low-dose 5-azacytidine (5-aza) daily for either 5 or 10 days, in combination with durvalumab and tremelimumab. The primary objective was to determine the biologically effective dose of 5-aza. In this study, RNA sequencing (RNA-seq) was performed on baseline and on-treatment samples from eight participants, and transcriptomic changes were analyzed to assess the impact of low-dose 5-aza treatment.

  Study EGAS50000000728

• PCa-LINES

  PCa-LINES: Ribo-minus RNA-seq of 4 patient samples and 2 PCa cell lines ---- Detection of fusion transcripts and their genomic breakpoints from RNA sequencing data Youri Hoogstrate, Malgorzata A. Komor, René Böttcher, Job van Riet, Harmen J. G. van de Werken, Stef van Lieshout, Ralf Hoffmann, Evert van den Broek, Anne S. Bolijn, Natasja Dits, Daoud Sie, David van der Meer, Floor Pepers, Chris H. Bangma, Geert J. L. H. van Leenders, Marcel Smid, Pim French, John W.M. Martens, Wilbert van Workum, Peter J. van der Spek, Bart Janssen, Eric Caldenhoven, Christian Rausch, Mark de Jong, Andrew P. Stubbs, Gerrit A. Meijer, Remond J.A. Fijneman, Guido Jenster bioRxiv 2021.05.17.441778; doi: https://doi.org/10.1101/2021.05.17.441778 https://www.biorxiv.org/content/10.1101/2021.05.17.441778v1

  Study EGAS00001004613

• Exome-seq, RNA-Seq, SNP array profiling of gastric tumor samples and cell lines.

  Gastric cancer is the second leading cause of worldwide cancer mortality, yet the underlying genomic alterations remain poorly understood. Here we performed exome and transcriptome sequencing and SNP array assays to characterize 51 primary gastric tumors and 32 cell lines. Meta-analysis of the exome data and previously published data sets revealed 24 significantly mutated genes in MSS tumors, and 16 in MSI tumors. More than half of the patients in our collection could potentially benefit from targeted therapies. We identified 55 splice-site mutations accompanied by aberrant splicing products, in addition to mutation-independent differential isoform usage in tumors. The ZAK kinase isoform TV1 is preferentially upregulated in gastric tumors and cell lines relative to normal samples. This pattern is also observed in colorectal, bladder, and breast cancers. Overexpression of this particular isoform activated multiple cancer-related transcription factor reporters, while depletion of ZAK in gastric cell lines inhibited proliferation. These results reveal the spectrum of genomic and transcriptomic alterations in gastric cancer, and identify isoform-specific oncogenic properties of ZAK.

  Study EGAS00001000736

• atrial appendage RNA-seq in non-, paroxysmal and persistent atrial fibrillation

  Understanding the interconnectedness of structural remodelling processes atrial fibrillation (AF) in patients could identify targets for future therapies. These data include transcriptome sequencing of atrial tissues of patients without AF, with paroxysmal AF and persistent AF (total n=64). In AF patients, epicardial cell gene expression decreased, contrasting with an upregulation of epithelial to mesenchymal transition (EMT) and mesenchymal cell gene expression. Immunohistochemistry demonstrated thickening of the epicardium and an increased proportion of (myo)fibroblast-like cells in the myocardium, supporting enhanced EMT in AF. We furthermore report an upregulation of endothelial cell proliferation, angiogenesis and endothelial signalling. EMT and endothelial cell proliferation concurred with increased interstitial (myo)fibroblast-like cells and extracellular matrix gene expression including enhanced tenascin-c, thrombospondins, biglycan and versican. Morphological analysis discovered increased and redistributed glycosaminoglycans and collagens in the atria of AF patients. Signalling pathways, including cell-matrix interactions, PI3K-AKT and Notch signalling, that could regulate mesenchymal cell activation, were upregulated. These dynamic processes may provide targets to prevent or reverse structural remodelling.

  Study EGAS00001005295

• NIBIT-EPI-MESO study samples

  Multi-omics analysis of pre-immuno checkpoint inhibitors (ICI) therapy lesions from 91 pleural mesothelioma (PM) patients enrolled in the multicenter NIBIT-EPI-MESO study. Neoplastic lesions were characterized using multiple molecular platforms, including RNA sequencing (n=82), Whole Exome Sequencing (WES) (n=87), Reduced Representation Bisulfite Sequencing (RRBS) (n=83) and cell-free methylated immunoprecipitation sequencing (cfMeDIP-seq) (n=18). Tumor samples were collected during the standard diagnostic pleuroscopy or thoracoscopy before ICI therapy. Matched Peripheral Blood Mononuclear Cells (PBMC) were collected from PM patients before ICI therapy.

  Study EGAS50000001478

• Genomic Landscape of Pediatric Myelodysplastic Syndromes

  Pediatric myelodysplastic syndromes (MDS) are a rare disease and unlike their adult counterpart, very little is known about their genomic landscape. We characterized a cohort of patients from a single institution by whole exome sequencing, as well as a subset of patients by whole genome sequencing, RNA-sequencing and targeted deep sequencing. We found a spectrum of mutations, both somatic and germline, that are distinct from those observed in adult MDS. In turn, we observed mutations commonly observed in other pediatric myeloid tumors.

  Study EGAS00001002202

• Triple Negative Breast Cancer RNA Sequencing

  We propose to definitively characterise the somatic genetics of triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Dataset EGAD00001000390

• Integrating Genomic and Transcriptomic Data to Identify Breast Cancer Susceptibility Genes

  Genetic factors play an important role in the etiology of both sporadic and familial breast cancer. Since 2007, common genetic variants in ~200 loci have been identified in genome-wide association studies (GWAS) in relation to breast cancer risk. However, it is often difficult to translate GWAS findings to disease prevention and treatment since causal genes in the large majority of GWAS-identified loci are unknown. Furthermore, a large fraction of breast cancer heritability remains unexplained. Recent studies suggest that nearly 80% of disease heritability can be explained by genetic variants regulating gene expression. Herein, we propose three well-powered transcriptome-wide association studies (TWAS) to systematically investigate the association of breast cancer risk with gene expression across the transcriptome of African, Asian and European descendants. In Aim 1, we will perform RNA sequencing and high-density genotyping assays using normal breast tissue samples, and build race-specific gene expression prediction models using data from 1000 women of African, Asian and European descent. These models will be applied to the GWAS data generated from approximately 320,000 breast cancer patients and controls to impute gene expression for association analyses of predicted gene expression with risk of breast cancer overall, and by estrogen receptor and HER2 status. In Aim 2, we will select the top 50 genes identified in Aim 1 for in vitro functional assays to assess their influence on major cell functions related to cancer biology. In Aim 3, we will evaluate whether TWAS-identified genes may express differently in normal breast tissues and breast cancer tissues collected from African, Asian, and European descendants to assess whether these genes may contribute to racial differences in breast cancer risk by molecular subtypes. With strong methodology and a large sample size, we believe that this proposed study should be able to identify and characterize a large number of novel genes related to breast cancer risk. Uncovering breast cancer susceptibility genes will greatly improve the understanding of the genetic and biological basis for breast cancer and accelerate the translation of genetic findings to disease prevention and patient care.

  Study phs003535

• Metatranscriptomic Sequencing of Pre-Transplant Bronchoalveolar Lavage in Pediatric Stem Cell Transplant Patients

  Children with malignancies, immunodeficiencies, and other life-threatening diseases sometimes receive allogeneic hematopoietic cell transplantation (HCT) as a treatment for their disease. The HCT process can be complicated by the development of lung disease from infection, alloreactivity, or other causes. To identify patients at-risk for post-HCT lung disease, this study uses metatranscriptomic RNA sequencing of bronchoalveolar lavage (BAL) obtained prior to HCT. Sequencing results are associated with the development of post-HCT lung injury. 

  Study phs002208

• RNA-sequencing of mechanical stress induced osteoarthritis-like damage in aged human cartilage explants treated with the anti-deiodinase iopanoic acid

  The current study aimed to confirm chondroprotective effects of the D2 inhibitor iopanoic acid (IOP) in an ex vivo aged human osteochondral explant model in which injurious mechanical stress is applied to inflict OA-like damage. This dataset contains RNA-seq (Illumina HiSeq X ten) of osteochondral explant cartilage from aged human patients that underwent a joint replacement surgery due to OA (N=10 donors; n=21 explants).

  Study EGAS00001006242